Can you use machine learning for binary data?
Of course you can use AI (specially Deep Learning) in your application. your covariates will be the input to your AI model and the model should predict probability of presence. The model has no problem with binary data and binary data is common in this field.
Also note that 1:100 ratio is not good and the network will probably learn to output absence for any input (this way it gets 99% accuracy but really it's not doing anything). So you should probably balance them (using almost same data, or telling network to pay more attention to presence data (by weighting the related loss)).
I think nowdays you can find Deep Learning in any popular coding language. But most of DL community use python and its really easy to learn.
If you want to learn Deep Learning there are a lot of sources on internet. But I suggest you the Deep Learning courses of Deeplearning.ai in coursera (If you have a lot of time) and CS231n of Stanford university on youtube (If you have time)